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The talks, the first concrete move toward negotiating an end to two months of civil unrest, ended after about three hours, but there was no immediate word from the presidency. Opposition leaders said they would give a report on the talks later to their supporters rallying on Kiev's central Independence Square.
Two of the dead men perished from bullet wounds, Ukraine's general prosecutor said, and the third died after plunging from the top of Dynamo football stadium while fighting with police.
They were the first protest-related deaths since the crisis erupted last November after Yanukovich ditched a trade deal with the European Union in favour of financial aid from Soviet-era overlord Russia to prop up Ukraine's ailing economy.
The protesters, inflamed by news of the deaths, faced off again with riot police, whom they have battled in bloody clashes near the government headquarters since Sunday night.
Though repelled by forays of baton-wielding riot police, they continued to return to the spot, setting tyres ablaze and sending clouds of black smoke wafting into police lines.
Fifty people were detained overnight and 29 of them were officially charged with taking part in mass unrest, police said. A total of 167 police have been injured, officials said. There was no estimate of the number of civilians injured.
Before going into the talks with opposition leaders, including boxer-turned-politician Vitaly Klitschko, former economy minister Arseny Yatsenyuk and far-right nationalist Oleh Tyahnibok, Yanukovich issued a statement deploring the loss of life.
Urging people not to heed the calls of "political radicals," Yanukovich said: "I am against bloodshed, against the use of force, against inciting enmity and violence."
Yanukovich has so far stood firm against opposition demands for the dismissal of Prime Minister Mykola Azarov's government and the prosecution of the interior minister, whom the protesters hold responsible for heavy-handed police tactics.
The meeting with Yanukovich marked a small victory for the three leaders who had sought his direct participation in talks.
But with some radical protesters ignoring pleas for non-violent action, it seemed unlikely opposition leaders would be satisfied with a repetition of appeals from Yanukovich to rein in the demonstrators.
Taking a tough line that may still foreshadow a big police crackdown, Azarov told a cabinet meeting: "Terrorists from the 'Maidan' (Independence Square) seized dozens of people and beat them. I am officially stating that these are criminals who must answer for their action."
He blamed opposition leaders for inciting "criminal action" by backing the anti-government protests, which he said had destabilised Ukraine, a country of 46 million people.
The Kiev demonstrations turned more violent on Sunday after harsher police tactics and the introduction of sweeping anti-protest legislation which the opposition says paved the way for a police state in the former Soviet republic.
Though hundreds of people have continued to protest peacefully in an encampment on Independence Square, a smaller group of hardcore radicals have now effectively hijacked the movement by attacking police with petrol bombs, fireworks and cobblestones. Police have replied with rubber bullets, stun grenades and tear gas.
Azarov said that police deployed on the streets did not possess firearms and the Interior Ministry has denied that police have used guns during the crisis.
U.S. REVOKES VISAS
In a move underlining Washington's disapproval of Ukraine's handling of the protests, the U.S. Embassy in Kiev said it had revoked the visas of several Ukrainians linked to police violence against the demonstrators in November and December.
It did not name the officials, but said it was considering further action against those responsible for the current violence.
In Washington, a State Department spokeswoman said the United States strongly condemned the violence, as well as "the targeted attacks against journalists and peaceful protesters."
"We urge all sides to immediately de-escalate the situation and refrain from violence," spokeswoman Marie Harf said in a statement.
Harf blamed increasing tensions in Ukraine on anti-democratic measures taken by the government, but also said the extreme-rightist group Pravy Sektor was inflaming tensions.
The European Union called on Ukraine's government and opposition to "engage in a genuine dialogue."
"I strongly condemn the violent escalation of events in Kiev overnight leading to casualties. The reported deaths of several protesters are a source of extreme worry," EU foreign policy chief Catherine Ashton said in a statement.
European Commission President Jose Manuel Barroso said the EU could also take action against Ukraine after reports of the overnight deaths.
With the opposition calling for a fresh rally on Wednesday, many shops, businesses and bank branches said they were closing early out of fear of more unrest.
Even as Yanukovich and opposition leaders met, black-helmeted riot police launched another operation to push back protesters, using an armoured personnel carrier.
But the police operation stopped well short of Independence Square, crucible of the so-called Euro-Maidan protests.
Wednesday's violence erupted ironically as Ukraine marked National Unification Day - the day in 1919 which brought together that part of the country that had been under Russian rule with that which had been in the Austro-Hungarian empire.